'Please explain': Johnathan Thurston and the Cowboys have asked the NRL for an explanation on the controversial no-try call made in golden point to deny the Cowboys a win against Brisbane. Photo: Getty Images

However, it seems there are some teething problems after Cowboys coach Paul Green confirmed he would be issuing a strong 'please explain' to the league over not one but three game-changing calls.

North Queensland were left to rue a dubious obstruction call that denied them a 65th-minute try, an 82nd minute forward pass and Johnathan Thurston being denied a match-winning golden point try over a contentious knock-on.

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Brisbane master coach Wayne Bennett had forewarned the league, saying the new bunker system would not be perfect despite the NRL hype.

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But that did not make it any easier for the Cowboys to digest some major calls that went against them at a sold out Suncorp Stadium on Friday night.

Green's biggest issue was Michael Morgan being denied a 65th minute try that would have given the visitors the lead for the first time due to a contentious obstruction call.

The bunker claimed backrower Ethan Lowe took out Brisbane's Alex Glenn in the lead-up.

"He [Glenn] would never have got there," Green said.

"It [Lowe's hit] would have made no impact on the play whatsoever."

Then there was Cowboys co-captain Thurston's disallowed 84th minute try.

Thurston appeared to score the golden point match-winner by pouncing on a loose ball batted back from the sidelines by diving winger Kyle Feldt.

However, the bunker saw a knock on in the lead-up - not that they would elaborate on who did it afterwards.

Thurston was seen arguing with officials after Anthony Milford kicked his 40m match-winning field goal in the 85th minute just moments after the Cowboys half was denied his four-pointer.

"I was just asking for an explanation and as usual they couldn't give it to me," Thurston said.

"Feldt knocked it into his own foot so I don't know how that could be a knock on," Green said.

"I need to clarify that."

History appeared to be repeating in the 82nd minute when Morgan set up Feldt for a match winning sideline try just as he did in the 2015 season decider.

But this time the touch judge cut short the Cowboys celebrations by ruling a borderline forward pass - much to Green's frustration.

"I didn't think it was forward, no," Green said.

"We shouldn't be talking about decisions, we should be talking about the game."

Green wasn't the only coach upset with aspects of Friday night's blockbuster, with Bennett expressing displeasure with the penalties conceded by the Cowboys.

The master coach took exception to the Cowboys after Brisbane were gifted four penalties virtually in front of the uprights by the visitors.

Bennett accused the Cowboys of giving away two points rather than risk six by committing professional fouls when the Broncos were attacking 20m from the try-line.

He even claimed the NRL were "three years behind" in development due to what he believed was a blight on the game.

"[NRL boss] Todd [Greenberg] has said the game is in front of tactics, well we are about three years behind [after] the amount of penalties we got," Bennett said.

"They [professional fouls] haven't gone out of the game and there are certain teams that do it. Their mindset is 'it's better to give you two than give you six'."

"Not all clubs are into it, but we have to have a better ruling than getting kicks when giving penalties away. We want to play football in there, we don't want to be taking the two points to be honest. The game has to start having a look at it."